Rice Genetics IV - IRRI books - International Rice Research Institute

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Finnegan J, McElroy D. 1994. Transgene inactivation: plants fight back! Bio/Technology 12:883-888.Fitchden JH, Beachy RN. 1993. Genetically engineered protection against viruses in transgenicplants. Annu. Rev. Microbiol. 47:739-763.Flavell RB. 1994. Inactivation of gene expression in plants as a consequence of specific sequenceduplications. Proc. Natl. Acad. Sci. USA 91:3490-3496.Garcia JA, Cervera MT, Riechmann JL, Lopez-Otin C. 1993. Inhibitory effects of human cystatin-C on plum pox potyvirus proteases. Plant Mol. Biol. 22:697-701.Gerlach WL, Llewellyn D, Haseloff J. 1987. Construction of a plant disease resistance genefrom the satellite RNA of tobacco ringspot virus. Nature 328:802-805.Gibbs MJ, Waterhouse PM, Weiller GF. 1997. Analysis of natural viral recombination mayassist the design of new virus resistance traits. In: McLean GD, Waterhouse PM, Evans G,Gibbs MJ, editors. Commercialization of transgenic crops: risk, benefit and trade considerations.Proceedings of the workshop, 11-13 March 1997, Canberra, Australia. Canberra(Australia): Australian Government Publishing. p 159-172.Golemboski DB, Lomonossoff GP, Zaitlin M. 1990. Plants transformed with a tobacco mosaicvirus nonstructural gene sequence are resistant to the virus. Proc. Natl. Acad. Sci. USA87:6311-6315.Green PJ, Pines O, Inouye M. 1988. The role of antisense in gene regulation. Annu. Rev. Biochem.55:569-597.Harrison BD, Mayo MA, Baulcombe DC. 1987. Virus resistance in transgenic plants that expresscucumber mosaic virus satellite RNA. Nature 328:799-801.Haseloff J, Gerlach WL. 1988. Simple RNA enzymes with new and highly specificendoribonuclease activities. Nature 334:585-591.Hayakawa T, Zhu Y, Itoh K, Kimura Y, Izawa T, Shimamoto K, Toriyama S. 1992. Geneticallyengineered rice resistant to rice stripe virus, an insect-transmitted virus. Proc. Natl. Acad.Sci. USA 89:9865-9869.Herdt RW. 1991. Research priorities for rice biotechnology. In: Khush GS, Toenniessen GH,editors. Rice biotechnology. Manila (Philippines): International Rice Research Institute,and Wallingford (UK): CAB International. p 19-54.Huntley CC, Hall TC. 1996. Interference with brome mosaic virus replication in transgenicrice. Mol. Plant-Microbe Interact. 9:164-170.Koller A, Dalmay T, Burgyan J. 1993. Defective interfering RNA-mediated resistance againstcymbidium ringspot tombusvirus in transgenic plants. Virology 193:313-318.Kouassi N, Brugidou C, Chen L, Ngon M, Yassi A, Beachy RN, Fauquet CM. 1997. Transgenicrice plants expressing rice yellow mottle virus coat protein gene. Int. Rice Res. Notes 22:14-15.Lindbo JA, Dougherty WG. 1992. Pathogen-derived resistance to a potyvirus: immune andresistant phenotypes in transgenic tobacco expressing altered forms of a potyvirus coatprotein nucleotide sequence. Mol. Plant-Microbe Interact. 5:144-153.Lodge JK, Kaniewski WK, Tumer NE. 1993. Broad-spectrum virus resistance in transgenicplants expressing pokeweed antiviral protein. Proc. Natl. Acad. Sci. USA 90:7089-7093.Malyshenko SI, Kondakova OA, Nazarova JV. 1993. Reduction of tobacco mosaic virus accumulationin transgenic plants producing non-functional viral transport proteins. J. Gen.Virol. 74:1149-1156.Matsumura T, Tabayashi N. 1995. Transformation of rice plants by plant reovirus genes. Sem.Virol. 6:133-139.418 Upadhyaya et al
McLean GD, Evans G. 1997. Some potential benefits from the use of transgenic crops withresistance to non-selective herbicides in Australian farming systems. In: McLean GD,Waterhouse PM, Evans G, Gibbs MJ, editors. Commercialisation of transgenic crops: risk,benefit and trade considerations. Proceedings of a workshop, 11-13 March 1997, Canberra,Australia. Canberra (Australia): Australian Government Publishing. p 293-300.Miller WA, Koev G, Mohan BR. 1997. Are there risks associated with transgenic resistance toluteoviruses? Plant Dis. 81:700-710.Mueller E, Gilbert J, Devenport G, Brigneti G, Baulcombe DC. 1995. Homology-dependentresistance: transgenic virus resistance in plants related to homology-dependent gene silencing.Plant J. 7:1001-1013.Omura T. 1995. Genomes and primary protein structures of phytoreoviruses. Sem. Virol. 6:97-102.Osbourn JK, Watts JW, Beachy RN, Wilson TMA. 1989. Evidence that nucleocaspid disassemblyand a later step in virus replication are inhibited in transgenic tobacco expressing TMVcoat protein. Virology 172:370-373.Osbourn JK, Sarkar S, Wilson TMA. 1990. Complementation of coat protein-defective TMVmutants in transgenic tobacco plants expressing TMV coat protein. Virology 179:921-925.Pinto YM, Kok RA, Baulcombe DC. 1999. Resistance to rice yellow mottle virus (RYMV) incultivated African rice varieties containing RYMV transgenes. Nat. Biotechnol. 17:702-707.Powell-Abel PA, Nelson RS, De B, Hoffmann N, Rogers SG, Fraley RT, Beachy RN. 1986.Delay of disease development in transgenic plants that express the tobacco mosaic viruscoat protein gene. Science 232:738-743.Pressoir G, Albar L, Ahmadi N, Rimbault I, Lorieux M, Fargette D, Ghesquiere A. 1998. Geneticbasis and mapping of the resistance to rice yellow mottle virus. II. Evidence of acomplementary epistasis between two QTLs. Theor. Appl. Genet. 97:1155-1161.Qu RD, Bhattacharya M, Laco GS, DeKochko A, Rao BLS, Kaniewska MB, Elmer JS, RochesterDE, Smith CE, Beachy RN. 1991. Characterization of the genome of rice tungrobacilliform virus: comparison with Commelina yellow mottle virus and caulimoviruses.Virology 185:354-364.Ramasamy C, Jatileksono T. 1996. Intercountry comparison of insect and disease losses. In:Evenson RE, Herdt RW, Hossain M, editors. Rice research in Asia: progress and priorities.Manila (Philippines): International Rice Research Institute, and Wallingford (UK): CABInternational. p 305-316.Sanford JC, Johnston SA. 1985. The concept of parasite-derived resistance: deriving resistancegenes from the parasite’s own genome. J. Theor. Biol. 113:395-405.Sebastian LS, Ikeda R, Huang N, Imbe T, Coffman WR, McCouch SR. 1996. Molecular mappingof resistance to rice tungro spherical virus and green leafhopper. Phytopathology 86:25-30.Shen P, Kaniewska M, Smith C, Beachy RN. 1993. Nucleotide sequence and genomic organizationof rice tungro spherical virus. Virology 193:621-630.Sijen T, Wellink J, Hiriart JB, Van Kammen A. 1996. RNA-mediated virus resistance: role ofrepeated transgenes and delineation of targeted regions. Plant Cell 8:2277-2294.Sivamani E, Huet H, Shen P, Ong CA, deKochko A, Fauquet C, Beachy RN. 1999. Rice plants(Oryza sativa L.) containing rice tungro spherical virus (RTSV) coat protein transgenes areresistant to virus infection. Mol. Breed. 5:177-185.Engineering for virus resistance in rice 419
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Retrotransposons of rice as a tool
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First, the Rice Genetics Cooperativ
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OverviewRice genetics from Mendel t
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Rice genetics from Mendelto functio
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nese cultivar Nipponbare. The chrom
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Gene symbolization in riceIn the ab
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Table 2. Some examples of mapping g
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and YAC libraries, respectively. Th
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gene from wild species is the intro
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ReferencesAbbasi FM, Brar DS, Carpe
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Nagao S. 1951. Genic analysis and l
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Yoshimura S, Yamanouchi U, Katayose
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important traits for which segregat
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trolled by a single recessive gene,
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AromaAromatic rice varieties often
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Submergence tolerance is an interes
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Kinoshita T, Maekawa M. 1986. Genet
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NotesAuthors’ addresses: J.N. Rut
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The Rockefeller Foundation has a lo
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Evolution and implementation of the
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Scientific progress and outputsIn t
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Another salient example is that of
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BOX NO. 1recent international works
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For the purposes of this discussion
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Because of the great diversity (sci
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eeders where final products to enha
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Chen S, Lin XH, Xu CG, Zhang Q. 200
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Toenniessen GH. 1998. Rice biotechn
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Molecular markers,genetic diversity
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Evolution and domestication of rice
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ABCDO. barthiiO. rufipogonO. longis
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Wild(O. rufipogon)Geographical diff
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South Asia (particularly on the wes
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al 1992, Sun et al 1996a,b,c), thou
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wild and cultivated types (Est10, W
Page 87 and 88:
Cai HW, Morishima H. 2000a. Diversi
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Sato YI, Tang SX, Yang LU, Tang LH.
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The solid base laid by classical ri
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The synthesis shown in Figure 1 is
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Arabidopsis, long heralded as a “
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Monocots and eudicots: Is there sti
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Zhang H, Jia J, Gale MD, Devos KM.
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ility of rice productivity (Lu 1999
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Table 1 continuedIntrageneric class
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Molecular markers and evolutionary
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A100100521010078100991009894100O. s
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Two distinct types of sequences wer
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arthii and O. longistaminata, and t
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testing Ka/Ks between the homeologo
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Roschevicz RI. 1931. A contribution
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Miniature inverted repeattransposab
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eau and Wessler 1992, 1994), rice (
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MITEs as a source of allelic divers
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ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
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Le QH, Wright S, Yu Z, Bureau T. 20
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Microsatellite markers in rice:abun
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make the best SSR markers for rice.
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Predicted frequency100,00080,000Cla
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Relationship between SSRs and genes
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are indicated with RM locus designa
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SSRs have been used to define intro
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provide a bridge for moving rapidly
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Ishii T, McCouch SR. 2000. Microsat
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NotesAuthors’ addresses: S.R. McC
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traits of economic importance (Mack
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Table 2. Tagging and mapping of som
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even at the juvenile stage. Several
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Chen et al (2000) transferred the b
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genome sequence of rice, this will
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Kurata N, Nagamura Y, Yamamoto K, H
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Witcombe JR, Hash CT. 2000. Resista
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QTL mapping in rice:a few critical
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M-QTLsM-QTLs are defined as single
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(genetic/statistical models and cor
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Table 5. The percentage of three ty
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Table 7. Some environment-specific
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ferently to the environments. Simil
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(case 3), one may infer that this g
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Simultaneous QTL introgression and
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Doebley J, Stec A, Gustus C. 1995.
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Visscher PM, Haley CS, Thompson R.
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unavailable until recently with the
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Table 1 continued.Trait QTL a Flank
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the remaining parts of the linkage
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Table 3. QTLs detected for yield an
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Table 6. Correlations of various pa
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The functions of these sequences ne
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Structural and functional genomicsT
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The International Rice GenomeSequen
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the RGP, a PAC (P1-derived artifici
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Progress of sequencing in the RGPWe
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ice genome sequencing to organize a
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Strategies and techniquesfor finish
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uses the quality values generated b
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with the advanced techniques requir
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times contain sufficient data to ma
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amplification of regions that previ
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4. Structure problems—subcloning
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estriction maps or optical maps are
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nal assembly may point to areas tha
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McMurray AA, Sulston JE, Quail MA.
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Sequence-tagged connector/DNA finge
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1999). The development of multiple-
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Transposable elements in the rice H
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ers, maps, mapping populations, and
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Miropeats-OSJNBa0065H03 1.2 cMThres
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NotesAuthors’ addresses: R.A. Win
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Sasaki 1997). Such analysis is ofte
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ABNipponbare × KasalathF 2QTL anal
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were classified into two groups bas
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effective at determining the genoty
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addition, some accessions of wild r
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Sasaki T, Burr T. 2000. Internation
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Mutational analysis has long been t
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marked by a deletion/chromosomal re
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analysis suggests that the mutation
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For drought-response screening, our
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Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
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Although mutants with discrete gene
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Generation of T-DNA insertionaltagg
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Aprobe AEEprobe BpGA1633RBgus Tn p3
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Number of loci36%224%170%010 20 30F
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Table 2. GUS assay in roots of tran
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1999, Krysan et al 1999, Sato et al
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Transposons and functionalgenomics
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cesses. To study the interactions a
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Constructs were made with the aim o
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RBcis-effect of the adjacent strong
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Ac knockout mutagenesisThe Ac lines
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Table 2 summarizes the transformati
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ReferencesBaldwin D, Crane V, Rice
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NotesAuthors’ addresses: R. Greco
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These include T-DNA (Azpiroz-Leehan
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polyproteins and two identical 138-
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mutant. The mutation in the ent-kau
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primers (G1, G2) and two Tos17-spec
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of insertion mutants by sequencing
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Grandbastien M-A, Spielman A, Caboc
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NotesAuthors’ addresses: H. Hiroc
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human endeavor, greatly contributed
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Equally important as the genomic in
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Oryzabase is one of the most recent
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Database structureA characteristic
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types of users. An annotation datab
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ReferencesAntonio BA, Fang Z, Sanch
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Gene isolation and functionEnhancin
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Enhancing deployment of genes forbl
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mochi and Tsuyuake (Wu et al 1996).
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tive indica rice varieties supports
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transcription factor, resulting in
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facilitate breeding durable resista
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(Inukai et al 1994, Yu et al 1996,
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Rossman AY, Howard RJ, Valent B. 19
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Molecular signaling in diseaseresis
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AOsRac1IED II III IV 214aaOsRac1 KC
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Japonica rice variety Kinmaze, whic
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Table 1. Characteristics of lesion-
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an effective inducer of host resist
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Takahashi A, Kawasaki T, Henmi K, S
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et al 2000). Sequence analysis of t
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612-amino acid protein, including t
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Genetic dissection of the Xa21-medi
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ReferencesAnderson PA, Lawrence GJ,
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Isolation of candidate genesfor tol
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Materials and methodsPlant material
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Microarray hybridization and data a
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Table 3. Most abundant transcripts
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Microarray technologyThe rapid accu
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view of procedures, pitfalls, and n
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Log(2) ratio1.51.0OC104E01—WCP1OC
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Table 5. Strongly regulated transcr
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ReferencesAdams MD, Soares MB, Kerl
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Acknowledgments: We thank Chris Bor
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y cells separating during tissue de
Page 380 and 381: (Erwee and Goodwin 1983). The sympl
Page 382 and 383: tion between the abundance of CDK t
Page 384 and 385: in a complex of 105 kDa. These resu
Page 386 and 387: Drew MC, Jackson MB, Giffard S. 197
Page 388 and 389: Umeda M, Umeda-Hara C, Yamaguchi M,
Page 390 and 391: asexual reproduction through apomix
Page 392 and 393: MPManual pollination by breeders×
Page 394 and 395: Search for apomixis in riceThere ar
Page 396 and 397: Issues related to achieving synthet
Page 398 and 399: come and may use imprinting to achi
Page 400 and 401: Embryo-inducing geneInactive ablati
Page 402 and 403: M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
Page 404 and 405: embryos, several genes characterist
Page 406 and 407: Our search for a rice homologue of
Page 408 and 409: sequenced the two rice DMC1 genes a
Page 410 and 411: Gustine DL, Sherwood RT, Huff DR. 1
Page 412 and 413: Peel MD, Carman JG, Leblanc O. 1997
Page 415 and 416: TransformationEngineering for virus
Page 417 and 418: Engineering for virusresistance in
Page 419 and 420: proteins, (2) the expression of dys
Page 421 and 422: Antisense and cosuppression RNA. Ex
Page 423 and 424: Table 1. Transgenic rice with patho
Page 425 and 426: the disease symptoms. Efforts from
Page 427 and 428: an ambisense coding strategy (Fig.
Page 429: first produced and shown to have vi
Page 433: Waterhouse PM, Upadhyaya NM. 1998.
Page 436 and 437: duction in response to dehydration
Page 438 and 439: (KIKEKLPG) in the carboxyl terminus
Page 440 and 441: These three plasmids were used to t
Page 442 and 443: We now show the effects of the toba
Page 444 and 445: Since one major goal of plant scien
Page 446 and 447: Table 4. Copy number of transgenes
Page 448 and 449: Chan M-T, Chang H-H, Ho S-L, Tang W
Page 450 and 451: NotesAuthors’ address: Department
Page 452 and 453: initially fixed by phosphoenolpyruv
Page 454 and 455: High-level expression of maize C 4-
Page 456 and 457: The effect of illumination on PPDK
Page 458 and 459: ate in 2% O 2 can be limited by Pi
Page 461 and 462: Transgene integration,organization,
Page 463 and 464: duced by organogenesis, somatic emb
Page 465 and 466: ing transgene organization. FISH an
Page 467 and 468: ments and the integration of exogen
Page 469 and 470: Level 2: activation of local repair
Page 471 and 472: strongly suggested that plant facto
Page 473 and 474: other cases it was not. We observed
Page 475 and 476: Gorbunova V, Levy AA. 1997. Non-hom
Page 477 and 478: Gene silencing and itsreactivation
Page 479 and 480: Carbofuran (trade name, Furadan) is
Page 481 and 482:
Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
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ABCDhptuidAmUbi1kb10.08.05.04.13.0F
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Fig. 4. X-gluc staining of germinat
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eflect different causes for silenci
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Table 4. Suppressors of silencing f
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Garrick D, Fiering S, Martin DI, Wh
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Xu Y, Buchholz WG, DeRose RT, Hall
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Rice molecular breeding workshopThi
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the working group can develop a net
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Rice genetics cooperativeA meeting
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